Table 2 Cryo-EM data collection, refinement, and validation statistics.
#1 SPike-SB23 1-up (EMDB-11616) (PDB 7A25) | #2 SPIKE-SB23 2-UP (EMDB-11617) (PDB 7A29) | |
|---|---|---|
Data collection and processing | ||
Magnification | 165,000x | – |
Voltage (kV) | 300 kV | – |
Electron exposure (e−/Å2) | 50 | – |
Defocus range (μm). | 0.3–1.1 | – |
Pixel size (Å). | 0.51 Å | – |
Symmetry imposed | C1 | – |
Initial particle images (no.) | 387,116 | – |
Final particle images (no.) | 70,854 | 69,567 |
Map resolution (Å) | 3.1 | 2.9 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.1–7.5 Å (FSC 0.143) | 2.1–7.2 Å (FSC 0.143) |
Refinement | ||
Initial model used (PDB code) | 6VSB, 6LZG, 4PFE | 6VSB, 6LZG, 4PFE |
Model resolution (Å) | 3.1 Å | 2.9 Å |
FSC threshold | 0.5 | 0.5 |
Model resolution range (Å) | 230–3.1 | 250–2.9 |
Map sharpening B factor (Å2) | −57 | −62 |
Model composition | ||
Non-hydrogen atoms | 28266 | 28286 |
Protein residues | 3504 | 3510 |
Ligands | 63 (NAG) | 61 (NAG) |
B factors (Å2) | ||
Protein | 82 | 115 |
Ligand | 107 | 125 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.003 | 0.002 |
Bond angles (°) | 0.672 | 0.531 |
Validation | ||
MolProbity score | 1.96 | 1.68 |
Clashscore | 7.85 | 7.95 |
Poor rotamers (%) | 2.08 | 0.03 |
Ramachandran plot | ||
Favored (%) | 95.76 | 96.29 |
Allowed (%) | 4.24 | 3.71 |
Disallowed (%) | 0.00 | 0.00 |
